All that mentioned by Rezard, still most games will need to have speedhacks enabled (play with the EE Cyclerate and VU Cycle Stealing). be aware than some games accept them nicely while other may not work nicely at all with them.

At the moment the emulator is unable to make use of all cores (I confess being a bit confused about your actual specs, it seems to be a double CPU motherboard with two Xeon that should perform like the 9400, still it does not matter that much in this particular case). The devs are trying to distribute the load but it's not ease because the PS2 pipeline architecture does not help in this.

Your video card can run many games at better resolution, go native only if absolutely necessary, use your judgement.

That's the better we can say to help generic configuration. Each PS2 game has it's own "minimal requirements" on the machine specs emulating it as PC games do. So, telling us the game you are playing at the moment is useful to know what specifics hacks and options to use.

A few games will run slowly does not matter what is tried, they are just too demanding.

One last advice, disable the vertical synch in your Nvidia control panel, it is known as responsible to cap the FPS in values that can be as low as half the monitor refresh rate or even less if this value can't be achieved, this is valid for PC games too. Although PC games may feel smooth running at 30 FPS, this is killing on console games under TV standards which have timing and synchronization tied to FPS.